Agricultural non-point source pollution (AGNPS) is currently a ubiquitous environmental problem throughout the world. Models are the main method used in research on non-point source pollution. The SWAT (Soil and Water Assessment Tool) model of AGNPS has been attracting increasing attention from governments and researchers. To gain a comprehensive understanding of the SWAT model of AGNPS research, we use a citation analysis tool for data mining to map scientific knowledge and determine the developmental trends, strengths, and hotspots of research using this model. The first SWAT model research paper was published in 1994, and since then the number of papers published on research with this model has risen each year. The United States is the definitive leader in research in this area. The amount of published papers from China was 407, which ranked it second among all of the world’s countries. In China, the Chinese Academy of Sciences and Beijing Normal University were prominent participants in studies using the SWAT model. Research hotspots mainly focused on the characteristics, evolution, algorithms, and applications of the SWAT model to AGNPS. The SWAT model is applied in the studies on major river basins abroad and many river basins in China. The SWAT model has been widely used in the studies on AGNPS, sediment yields and pesticide transportation. To provide an effective decision support tool and a scientific basis for watershed management and pollution control, in the future studies should actively carry out fundamental research on AGNPS while also designing special application elements of the SWAT model suitable for the varied watersheds of China.